RDKit
Open-source cheminformatics and machine learning.
Embedder.h File Reference
#include <map>
#include <Geometry/point.h>
#include <GraphMol/ROMol.h>

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Classes

struct  RDKit::DGeomHelpers::EmbedParameters
 Parameter object for controlling embedding. More...
 

Namespaces

 RDKit
 Includes a bunch of functionality for handling Atom and Bond queries.
 
 RDKit::DGeomHelpers
 

Functions

int RDKit::DGeomHelpers::EmbedMolecule (ROMol &mol, unsigned int maxIterations=0, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, const std::map< int, RDGeom::Point3D > *coordMap=0, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0)
 Compute an embedding (in 3D) for the specified molecule using Distance. More...
 
void RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs=10, int numThreads=1, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=0, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0)
 
INT_VECT RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, unsigned int numConfs=10, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=0, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0)
 
int RDKit::DGeomHelpers::EmbedMolecule (ROMol &mol, const EmbedParameters &params)
 
void RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs, const EmbedParameters &params)
 
INT_VECT RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, unsigned int numConfs, const EmbedParameters &params)
 

Variables

const EmbedParameters RDKit::DGeomHelpers::KDG
 Parameters corresponding to Sereina Riniker's KDG approach. More...
 
const EmbedParameters RDKit::DGeomHelpers::ETDG
 Parameters corresponding to Sereina Riniker's ETDG approach. More...
 
const EmbedParameters RDKit::DGeomHelpers::ETKDG
 Parameters corresponding to Sereina Riniker's ETKDG approach. More...